Life sciences · Preprint
arXiv · October 13, 2026
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Message passing neural networks have shown remarkable performance in algorithmic and constraint reasoning, due to their ability to encode the structure of the task directly in the architecture. Recent work has shown that better results can be achieved using recursive transformers trained with deep supervision and truncated recursions, which make extremely deep loops stable to train, and equipped with test-time procedures such as discrete deduction lattices. In this work, we apply the same procedures to message passing networks, and show that the two ingredients are complementary, and lead to parameter efficient models: we obtain about $99\%$ test accuracy on Sudoku-Extreme with a model of $16$k parameters that trains in about $10$ minutes on an H100, or in $9$ hours on a CPU. We further show that the cost of truncating gradients grows with the number of rounds information needs to cross the graph, making the choice of wiring a trade-off between robustness to truncation and transfer across problem sizes. We conclude by showing that our models transfer zero-shot to larger instances than those seen during training, outperforming popular neural baselines on N-queens and Boolean satisfiability with a fraction of their parameters.